Nicola Zamboni

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
    Ari Rantanen
    Department of Computer Science, University of Helsinki, Finland
    BMC Bioinformatics 9:266. 2008
  2. pmc Model-independent fluxome profiling from 2H and 13C experiments for metabolic variant discrimination
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Genome Biol 5:R99. 2004
  3. ncbi Differential glucose repression in common yeast strains in response to HXK2 deletion
    Anne Kümmel
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    FEMS Yeast Res 10:322-32. 2010
  4. ncbi Transient expression and flux changes during a shift from high to low riboflavin production in continuous cultures of Bacillus subtilis
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Biotechnol Bioeng 89:219-32. 2005
  5. doi 13C metabolic flux analysis in complex systems
    Nicola Zamboni
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Curr Opin Biotechnol 22:103-8. 2011
  6. doi The integrated response of primary metabolites to gene deletions and the environment
    Jennifer Christina Ewald
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Mol Biosyst 9:440-6. 2013
  7. pmc The Bacillus subtilis yqjI gene encodes the NADP+-dependent 6-P-gluconate dehydrogenase in the pentose phosphate pathway
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, Zurich, Switzerland
    J Bacteriol 186:4528-34. 2004
  8. doi Dynamic flux responses in riboflavin overproducing Bacillus subtilis to increasing glucose limitation in fed-batch culture
    Martin Rühl
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Str 16, CH 8093 Zurich, Switzerland
    Biotechnol Bioeng 105:795-804. 2010
  9. doi (13)C-based metabolic flux analysis
    Nicola Zamboni
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Nat Protoc 4:878-92. 2009
  10. doi Cross-platform comparison of methods for quantitative metabolomics of primary metabolism
    Jörg Martin Büscher
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Anal Chem 81:2135-43. 2009

Collaborators

Detail Information

Publications30

  1. pmc An analytic and systematic framework for estimating metabolic flux ratios from 13C tracer experiments
    Ari Rantanen
    Department of Computer Science, University of Helsinki, Finland
    BMC Bioinformatics 9:266. 2008
    ....
  2. pmc Model-independent fluxome profiling from 2H and 13C experiments for metabolic variant discrimination
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Genome Biol 5:R99. 2004
    ..The approach is flexible and paves the way to large-scale fluxome profiling of any biological system and condition...
  3. ncbi Differential glucose repression in common yeast strains in response to HXK2 deletion
    Anne Kümmel
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    FEMS Yeast Res 10:322-32. 2010
    ....
  4. ncbi Transient expression and flux changes during a shift from high to low riboflavin production in continuous cultures of Bacillus subtilis
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, CH 8093 Zurich, Switzerland
    Biotechnol Bioeng 89:219-32. 2005
    ..With the possible exception of a slight down-regulation of the purine biosynthesis pathway, genome-wide expression analysis indicated that transcriptional regulation was not responsible for the production decline...
  5. doi 13C metabolic flux analysis in complex systems
    Nicola Zamboni
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Curr Opin Biotechnol 22:103-8. 2011
    ..In the future, this practice will be complemented by novel modeling frameworks to assay particular fluxes within a network by stable isotopic tracer for targeted validation of well-defined hypotheses...
  6. doi The integrated response of primary metabolites to gene deletions and the environment
    Jennifer Christina Ewald
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Mol Biosyst 9:440-6. 2013
    ..Key biosynthetic precursors and cofactors were generally robust under all tested perturbations in spite of changes in fluxes and growth rate...
  7. pmc The Bacillus subtilis yqjI gene encodes the NADP+-dependent 6-P-gluconate dehydrogenase in the pentose phosphate pathway
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, Zurich, Switzerland
    J Bacteriol 186:4528-34. 2004
    ....
  8. doi Dynamic flux responses in riboflavin overproducing Bacillus subtilis to increasing glucose limitation in fed-batch culture
    Martin Rühl
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Str 16, CH 8093 Zurich, Switzerland
    Biotechnol Bioeng 105:795-804. 2010
    ..As a consequence, higher catabolic NADPH formation occurred than was necessary to satisfy the anabolic demands, suggesting a transhydrogenase-like mechanism to close the balance of reducing equivalents...
  9. doi (13)C-based metabolic flux analysis
    Nicola Zamboni
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Nat Protoc 4:878-92. 2009
    ..The presented protocols take 5-10 d, have been used extensively in the past decade and are exemplified here for the central metabolism of Escherichia coli...
  10. doi Cross-platform comparison of methods for quantitative metabolomics of primary metabolism
    Jörg Martin Büscher
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Anal Chem 81:2135-43. 2009
    ..Therefore, suitable internal standards, such as (13)C-labeled biomass extracts, are mandatory for quantitative metabolomics with any methods...
  11. doi Screening of Bacillus subtilis transposon mutants with altered riboflavin production
    Simon Tännler
    Institute of Molecular Systems Biology, ETH Zurich, CH 8093 Zurich, Switzerland
    Metab Eng 10:216-26. 2008
    ..This improvement was also verified under the more process-relevant conditions of a glucose-limited fed-batch culture...
  12. ncbi The phosphoenolpyruvate carboxykinase also catalyzes C3 carboxylation at the interface of glycolysis and the TCA cycle of Bacillus subtilis
    Nicola Zamboni
    Institute of Biotechnology, Swiss Federal Institute of Technology Zurich ETH ETH Zürich, Zurich 8093, Switzerland
    Metab Eng 6:277-84. 2004
    ..Presumably as a consequence of the unfavorable kinetics of an ATP-synthesizing anaplerotic PEP carboxykinase reaction, such pyruvate carboxylase mutants grow slowly or, as in the case of wild-type 168, not at all...
  13. doi Collisional fragmentation of central carbon metabolites in LC-MS/MS increases precision of ¹³C metabolic flux analysis
    Martin Rühl
    Institute of Molecular Systems Biology, ETH Zurich, Dr Nicola Zamboni, Wolfgang Pauli Str 16, CH 8093 Zurich, Switzerland
    Biotechnol Bioeng 109:763-71. 2012
    ..In the future, this catalogue will enable comprehensive in silico calculability analyses to identify the most sensitive measurements and direct experimental design...
  14. pmc Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity
    Sarah Maria Fendt
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Mol Syst Biol 6:356. 2010
    ..Hence, alteration in one network constituent can be efficiently buffered by converse alterations in the other constituent, implying a passive mechanism to maintain metabolic homeostasis upon perturbations in enzyme capacity...
  15. ncbi Non-stationary (13)C-metabolic flux ratio analysis
    Manuel Hörl
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Str 16, 8093, Zurich, Switzerland PhD Program Systems Biology, Life Science Zurich Graduate School, Zurich, Switzerland
    Biotechnol Bioeng 110:3164-76. 2013
    ..Hence this approach paves the road to targeted (13)C-MFA in dynamic systems with multiple carbon sources and towards rich media...
  16. pmc FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, 8093 Zurich, Switzerland
    BMC Bioinformatics 6:209. 2005
    ..A conceptual simplification of flux analysis is the analytical determination of metabolic flux ratios exclusively from MS data, which can then be used in a second step to estimate absolute in vivo fluxes...
  17. pmc anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data
    Nicola Zamboni
    ETH Zurich, Institute of Molecular Systems Biology, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    BMC Bioinformatics 9:199. 2008
    ..So far, however, widespread application of NET analysis in metabolomics labs was hindered by the absence of suitable software...
  18. ncbi Knockout of the high-coupling cytochrome aa3 oxidase reduces TCA cycle fluxes in Bacillus subtilis
    Nicola Zamboni
    Institute of Biotechnology, ETH Zurich, CH 8093, Zurich, Switzerland
    FEMS Microbiol Lett 226:121-6. 2003
    ..Since the product-corrected biomass yields were identical in mutants and parent, the results show that efficient ATP generation is not overly important for exponential growth of B. subtilis in batch culture...
  19. pmc Engineering genetically encoded nanosensors for real-time in vivo measurements of citrate concentrations
    Jennifer C Ewald
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    PLoS ONE 6:e28245. 2011
    ..In a first in vivo application we show that E. coli maintains the capacity to take up glucose or acetate within seconds even after long-term starvation...
  20. ncbi High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints
    Eliane Fischer
    Institute of Biotechnology, ETH Zürich CH 8093, Zurich, Switzerland
    Anal Biochem 325:308-16. 2004
    ..coli shake flasks and 1-ml deep-well microtiter plates. Due to its simplicity, speed, and robustness, 13C-constrained metabolic flux balancing is promising for routine and high-throughput analysis on a miniaturized scale...
  21. ncbi Genetics. Getting closer to the whole picture
    Uwe Sauer
    Institute of Molecular Systems Biology, ETH Zurich, Switzerland
    Science 316:550-1. 2007
  22. doi Quantification and mass isotopomer profiling of α-keto acids in central carbon metabolism
    Michael Zimmermann
    Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
    Anal Chem 86:3232-7. 2014
    ..In conclusion, the here described method fills one of the last technical gaps for metabolomics investigations of central carbon metabolism. ..
  23. ncbi Novel biological insights through metabolomics and 13C-flux analysis
    Nicola Zamboni
    Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
    Curr Opin Microbiol 12:553-8. 2009
    ..Integration of metabolomics, (13)C-flux analysis and other data enable the condition-dependent characterization of regulatory circuits that ultimately govern the metabolic phenotype...
  24. doi Nontargeted profiling of coenzyme A thioesters in biological samples by tandem mass spectrometry
    Michael Zimmermann
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Anal Chem 85:8284-90. 2013
    ..This demonstrates the power of our method for untargeted profiling of CoA-thioesters and adds a missing link in mycobacterial cholesterol catabolism. ..
  25. doi High-throughput, accurate mass metabolome profiling of cellular extracts by flow injection-time-of-flight mass spectrometry
    Tobias Fuhrer
    Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
    Anal Chem 83:7074-80. 2011
    ..Finally, we present an exemplary screen with Escherichia coli deletion mutants to show the exquisite capacity of the platform to identify lesions in primary metabolism at high throughputs...
  26. ncbi Ultrahigh performance liquid chromatography-tandem mass spectrometry method for fast and robust quantification of anionic and aromatic metabolites
    Joerg Martin Buescher
    Institute of Molecular Systems Biology, ETH Zurich, Switzerland
    Anal Chem 82:4403-12. 2010
    ..5-50 mg dry cell weight. We recommend this method for routine and yet comprehensive quantification of primary metabolites in a wide variety of biological matrices...
  27. doi High-throughput quantitative metabolomics: workflow for cultivation, quenching, and analysis of yeast in a multiwell format
    Jennifer Christina Ewald
    Institute of Molecular Systems Biology, ETH Zurich, Wolfgang Pauli Strasse 16, 8093 Zurich, Switzerland
    Anal Chem 81:3623-9. 2009
    ..The described workflow allows the production of large amounts of metabolome samples within a day, is compatible with virtually all liquid extraction protocols, and paves the road to quantitative screens...
  28. ncbi Reducing maintenance metabolism by metabolic engineering of respiration improves riboflavin production by Bacillus subtilis
    Nicola Zamboni
    Institute of Biotechnology, Swiss Federal Institute of Technology Zurich, ETH Zurich, Honggerberg, CH 8093, Zurich, Switzerland
    Metab Eng 5:49-55. 2003
    ..The reduction of maintenance metabolism, in turn, significantly improved the yield of recombinant riboflavin and B. subtilis biomass in fed-batch cultures...
  29. pmc YtsJ has the major physiological role of the four paralogous malic enzyme isoforms in Bacillus subtilis
    Guillaume Lerondel
    Microbiologie et Genetique Moleculaire, INRA UMR1238 CNRS UMR2585 and INAP G, F 78850 Thiverval Grignon, France
    J Bacteriol 188:4727-36. 2006
    ..coli partially suppressed it. These results suggest an additional physiological role of YtsJ beyond that of malate-to-pyruvate conversion...
  30. ncbi Genome engineering reveals large dispensable regions in Bacillus subtilis
    Helga Westers
    Department of Pharmaceutical Biology, University of Groningen, Groningen, The Netherlands
    Mol Biol Evol 20:2076-90. 2003
    ..We show that genome engineering is a feasible strategy for functional analysis of large gene clusters, and that removal of dispensable genomic regions may pave the way toward an optimized Bacillus cell factory...